Package com.compomics.util.parameters.identification.tool_specific

Class PepnovoParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable
public class PepnovoParameters extends ExperimentObject implements IdentificationAlgorithmParameter
PepNovo specific parameters.
Author:
Marc Vaudel
See Also:

  • Constructor Details

    • PepnovoParameters

      public PepnovoParameters()
      Constructor.

  • Method Details

    • getHitListLength

      public Integer getHitListLength()
      Returns the length of the hit list.
      Returns:
      the length of the hit list

    • setHitListLength

      public void setHitListLength(Integer hitListLength)
      Sets the length of the hit list.
      Parameters:
      hitListLength - the length of the hit list

    • isEstimateCharge

      public Boolean isEstimateCharge()
      Indicates whether the precursor charge shall be estimated for PepNovo.
      Returns:
      a boolean indicating whether the precursor charge shall be estimated for PepNovo

    • setEstimateCharge

      public void setEstimateCharge(Boolean estimateCharge)
      Sets whether the precursor charge shall be estimated for PepNovo.
      Parameters:
      estimateCharge - a boolean indicating whether the precursor charge shall be estimated for PepNovo

    • isCorrectPrecursorMass

      public Boolean isCorrectPrecursorMass()
      Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
      Returns:
      a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

    • setCorrectPrecursorMass

      public void setCorrectPrecursorMass(Boolean correctPrecursorMass)
      Sets whether the precursor mass shall be corrected (TagDB setting).
      Parameters:
      correctPrecursorMass - a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

    • getDiscardLowQualitySpectra

      public Boolean getDiscardLowQualitySpectra()
      Returns a boolean indicating whether low quality spectra shall be discarded.
      Returns:
      a boolean indicating whether low quality spectra shall be discarded

    • setDiscardLowQualitySpectra

      public void setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
      Sets whether low quality spectra shall be discarded.
      Parameters:
      discardLowQualitySpectra - a boolean indicating whether low quality spectra shall be discarded

    • getFragmentationModel

      public String getFragmentationModel()
      Returns the name of the fragmentation model.
      Returns:
      the name of the fragmentation model

    • setFragmentationModel

      public void setFragmentationModel(String fragmentationModel)
      Sets the name of the fragmentation model.
      Parameters:
      fragmentationModel - the name of the fragmentation model

    • generateQuery

      public Boolean generateQuery()
      Returns a boolean indicating whether a blast query shall be generated.
      Returns:
      a boolean indicating whether a blast query shall be generated

    • setGenerateQuery

      public void setGenerateQuery(Boolean generateQuery)
      Sets a boolean indicating whether a blast query shall be generated.
      Parameters:
      generateQuery - a boolean indicating whether a blast query shall be generated

    • getPepNovoPtmMap

      public Map<String,String> getPepNovoPtmMap()
      Returns the PepNovo to utilities PTM map. Null if not set.
      Returns:
      the PepNovo to utilities PTM map, null if not set

    • getUtilitiesPtmName

      public String getUtilitiesPtmName(String pepnovoPtmName)
      Returns the utilities PTM name corresponding to the given PepNovo PTM name. Null if not found.
      Parameters:
      pepnovoPtmName - the PepNovo PTM name
      Returns:
      the utilities PTM name

    • setPepNovoPtmMap

      public void setPepNovoPtmMap(Map<String,String> pepNovoPtmMap)
      Set the PepNovo to utilities PTM map.
      Parameters:
      pepNovoPtmMap - the pepNovoPtmMap to set

    • getAlgorithm

      public Advocate getAlgorithm()
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the identification algorithm.
      Specified by:
      getAlgorithm in interface IdentificationAlgorithmParameter
      Returns:
      the identification algorithm

    • equals

      public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
      Description copied from interface: IdentificationAlgorithmParameter
      Indicates whether another identificationAlgorithmParameter has the same parameters.
      Specified by:
      equals in interface IdentificationAlgorithmParameter
      Parameters:
      identificationAlgorithmParameter - the other identificationAlgorithmParameter
      Returns:
      true if the algorithm and parameters are the same

    • toString

      public String toString(boolean html)
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the parameters as a string.
      Specified by:
      toString in interface IdentificationAlgorithmParameter
      Parameters:
      html - use HTML formatting
      Returns:
      the parameters as a string